Practicality of mitochondrial marker for diatoms community monitoring of the west coast of Korea

Abstract

The diatoms are ubiquitous and an important primary producer in coastal ecosystems. They are involved in carbon, nitrogen, and silicate exchanges between the water column and sediments as part of the biological pump. Despite of ecological importance of diatoms in mudflat, systematics and ecological studies have largely relied on morphological and ultrastructural characteristic and handful genes of nuclear and plastid i.e., LSU and SSU rRNAs, and rbcL. In present study, we used all available mitochondrial genomes (mtDNA) of diatoms from public DB (10 spp) and including newly determined mtDNAs, such as two benthic species, Berkeleya fennica TA424 GenBank accession NC_026126 (35,509 bp, 29.7% GC) and Navicula ramosissima TA439 NC_031848 (48,652 bp, 31.7% GC) isolated from the Taean, and one pelagic species, Skeletonema marinoi JK029 NC_028615 (38,515 bp, 29.7% GC) isolated from an intertidal site of the Sihwaho, the west coast of Korea. All CDS of mtDNAs were aligned and compared for new primer sets. Based on the statistical tests and preliminary sequencing by using culture strains, we selected three markers (cob, cox2, and nad5) for diatoms community monitoring on the west coast of Korea. We described and discussed new markers’ theoretical and practical utilities for diatoms monitoring based on preliminary results of field samples from the Geunsoman mudflat.mportance of diatoms in mudflat, systematics and ecological studies have largely relied on morphological and ultrastructural characteristic and handful genes of nuclear and plastid i.e., LSU and SSU rRNAs, and rbcL. In present study, we used all available mitochondrial genomes (mtDNA) of diatoms from public DB (10 spp) and including newly determined mtDNAs, such as two benthic species, Berkeleya fennica TA424 GenBank accession NC_026126 (35,509 bp, 29.7% GC) and Navicula ramosissima TA439 NC_031848 (48,652 bp, 31.7% GC) isolated from the Taean, and one pelagic species, Skeletonema marinoi JK029 NC_028615 (38,515 bp, 29.7% GC) isolated from an intertidal site of the Sihwaho, the west coast of Korea. All CDS of mtDNAs were aligned and compared for new primer sets. Based on the statistical tests and preliminary sequencing by using culture strains, we selected three markers (cob, cox2, and nad5) for diatoms community monitoring on the west coast of Korea. We described and discussed new markers’ theoretical and practical utilities for diatoms monitoring based on preliminary results of field samples from the Geunsoman mudflat.